The last two cases don't seem accurate . You may not kill an enemy nation and must allow those who want to run away the ability to do so (Mechilta in Parshas Masey)You never kill women and children and always allow those who want to accept surrender terms to do so . Even by the Shiva Ammim (see Rambam Hilchos Melochim Chapter six)
Some people may question how the rest of what the Rambam says there that fits with their current moral beliefs but in that context it must be realized that (among other things) you weren't dealing with people who followed the contemporary rules of war either.
You won't find the last paragraph in the Rishonim or even Achronim because they were written before things like the Geneva Convention and the current rules of war. It would only be latter day sources who would have an issue causing them to say it.
As far as giving a rape victim the right to force her rapist to marry her (but not the other way around of course) I'm not sure what the issue with that is even by today's standards.
As far as slavery is concerned there are a few sources dating from the mid 1800s who, with some variation, say that the Torah allowed (but did not encourage) slavery because in a situation where slavery is widespread it would be better even for the
slave himself to be owned by someone who has very strict limitations on how he may treat a slave (and even much stricter limitations on when he may acquire a slave who had once been a free man) than to be sold to anyone out there.
To give some perspective from my grandfather z'l who unlike anyone reading this WAS a slave : He never would have survived the six years of pure torture from when Germany invaded Poland until after WWII if not for two different few month periods when he was doing slave labor on some German commercial farm. The guy who owned the farm was no Tzadik and certainly did not follow the Torah's rules for treating an Eved Canaani. Let alone the Midas Chasidus for doing so heavily encouraged in Gemorah. But the guy also didn't kill, beat or starve his slave laborers. That "respite" allowed my grandfather the ability to "recuperate" and live. It was at that time that he came to realize that when slavery is rampant anyway you aren't doing anyone a favor by forbidding it for a limited group. Better let them have it with strict rules like the Torah does.